Changeset 6090

Timestamp:

Aug 22, 2012, 1:36:15 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1707: Make it possible for a derived bioassay to have multiple physical bioassays as parents

The 'Item overview' should now load parent items correctly. Validation need to be fixed (some parts have been disabled at the moment).

Location:

trunk/src/core/net/sf/basedb/util/overview

Files:

• Node.java (modified) (1 diff)
• loader/DerivedBioAssayLoader.java (modified) (10 diffs)
• loader/ExtractLoader.java (modified) (5 diffs)
• loader/PhysicalBioAssayLoader.java (modified) (4 diffs)
• validator/DerivedBioAssayValidator.java (modified) (2 diffs)

trunk/src/core/net/sf/basedb/util/overview/Node.java

@@ -286 +286 @@
   
   /**
+    Find all nodes in the parent chain that matches the given
+    filter.
+    @param filter The filter to use for matching nodes
+    @return A list with the matched nodes in the order they matched
+    @since 3.2
+  */
+  public List<Node> findAll(Filter<? super Node> filter)
+  {
+    List<Node> result = new LinkedList<Node>();
+    Node current = this;
+    while (current != null)
+    {
+      if (filter.evaluate(current)) result.add(current);
+      current = current.getParent();
+    }
+    return result;
+  }
+  
+  /**
     Get all child nodes of this node. May return null or an empty
     list if this node has no children.

trunk/src/core/net/sf/basedb/util/overview/loader/DerivedBioAssayLoader.java

@@ -21 +21 @@
 */
 package net.sf.basedb.util.overview.loader;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import net.sf.basedb.core.DbControl;
@@ -31 +35 @@
 import net.sf.basedb.core.PhysicalBioAssay;
 import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.core.Type;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.util.overview.Fix;
 import net.sf.basedb.util.overview.Node;
 import net.sf.basedb.util.overview.NodeAttribute;
 import net.sf.basedb.util.overview.OverviewContext;
-import net.sf.basedb.util.overview.cache.IndexedCacheKey;
-import net.sf.basedb.util.overview.filter.HasAttributeFilter;
+import net.sf.basedb.util.overview.OverviewUtil;
+import net.sf.basedb.util.overview.Validator;
 import net.sf.basedb.util.overview.filter.ItemTypeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
@@ -66 +73 @@
   {
     Node node = super.createRootNode(dc, context, item);
-    Extract extract = findExtract(null, item);
+    Extract extract = getExtract(item);
     if (extract != null) node.setAttribute(NodeAttribute.EXTRACT, extract);
     return node;
@@ -184 +191 @@
     ItemQuery<DerivedBioAssay> query = context.initQuery(bioAssay.getRootDerivedBioAssays(), "name");
     
-    // If there is an extract node in the parent chain we should only load
-    // derived bioassays with the same or a null extract
-    Node extractNode = bioAssayNode.getFirstNode(new ItemTypeFilter(Item.EXTRACT));
-    Extract extract = null;
-    if (extractNode != null)
-    {
-      extract = (Extract)extractNode.getItem();
-      query.restrict(Restrictions.or(
-          Restrictions.eq(Hql.property("extract"), Hql.entity(extract)), 
-          Restrictions.eq(Hql.property("extract"), null))
-        );
-    }
+    // We should only load derived bioassays that has a null extract or an
+    // extract that is found in the parent chain
+    Set<Integer> extractIds = getExtractChain(bioAssayNode);
+    if (extractIds.size() > 0)
+    {
+      query.restrict(
+        Restrictions.or(
+          Restrictions.eq(Hql.property("extract"), null),
+          Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
+        ));
+      query.setParameter("extracts", extractIds, Type.INT);
+    }
+
     ItemResultIterator<DerivedBioAssay> it = query.iterate(dc);
     while (it.hasNext())
@@ -204 +212 @@
         folderNode = new Node("bioassays", "Bioassays", bioAssayNode, ChildNodeDirection.FORWARD);
       }
-      Object cacheKey = new IndexedCacheKey(bioAssay, extract);
+      Object cacheKey = extractIds.size() > 0 ? null : child;
       createItemNode(nf, child, cacheKey, false, folderNode, ChildNodeDirection.FORWARD);
     }
@@ -222 +230 @@
     ItemQuery<DerivedBioAssay> query = context.initQuery(parent.getChildren(), "name");
     
-    // If there is an extract node in the parent chain we should only load
-    // derived bioassays with the same or a null extract
-    Node extractNode = parentNode.getFirstNode(new ItemTypeFilter(Item.EXTRACT));
-    Extract extract = null;
-    if (extractNode != null)
-    {
-      extract = (Extract)extractNode.getItem();
-      query.restrict(Restrictions.or(
-          Restrictions.eq(Hql.property("extract"), Hql.entity(extract)), 
-          Restrictions.eq(Hql.property("extract"), null))
-        );
+    // We should only load derived bioassays that has a null extract or an
+    // extract that is found in the parent chain
+    Set<Integer> extractIds = getExtractChain(parentNode);
+    if (extractIds.size() > 0)
+    {
+      query.restrict(
+        Restrictions.or(
+          Restrictions.eq(Hql.property("extract"), null),
+          Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
+        ));
+      query.setParameter("extracts", extractIds, Type.INT);
     }
 
@@ -243 +251 @@
         folderNode = new Node("bioassays", "Child bioassays", parentNode, ChildNodeDirection.FORWARD);
       }
-      Object cacheKey = new IndexedCacheKey(child, extract);
+      Object cacheKey = extractIds.size() > 0 ? null : child;
       createItemNode(nf, child, cacheKey, false, folderNode, ChildNodeDirection.FORWARD);
     }
@@ -263 +271 @@
     {
       bioAssay = raw.getParentBioAssay();
-      // We must clone/set the EXTRACT attribute so that upstream loaders
+      // We must set the EXTRACT attribute so that upstream loaders
       // follow the correct path when reaching the biomaterials section
-      if (bioAssay != null)
-      {
-        extract = findExtract(rawNode, bioAssay);
-      }
+      if (bioAssay != null) extract = getExtract(bioAssay);
     }
     catch (PermissionDeniedException ex)
@@ -274 +279 @@
       denied = true;
     }
-    Object cacheKey = new IndexedCacheKey(bioAssay, extract);
-    Node bioAssayNode = createItemNode(nf, bioAssay, cacheKey, denied, 
+    Node bioAssayNode = createItemNode(nf, bioAssay, null, denied, 
         rawNode, ChildNodeDirection.REVERSE);
     if (extract != null && bioAssayNode != null)
@@ -291 +295 @@
   {
     NodeFactory<DerivedBioAssay> nf = getNodeFactory(dc, context);
-    DerivedBioAssay bioAssay = null;
+    
+    ItemQuery<DerivedBioAssay> query = context.initQuery(child.getParents(), "name");
+    List<DerivedBioAssay> parents = query.list(dc);
+    
+    Node folderNode = null;
+    Node bioAssayNode = null;
+    if (parents.size() > 1)
+    {
+      folderNode = new Node("parents", "Parents", childNode, ChildNodeDirection.REVERSE);
+    }
+    
+    for (DerivedBioAssay dba : parents)
+    {
+      // We need to handle circular references inline because
+      // we can never require that a validator implementation handles this
+      Node circularNode = OverviewUtil.getCircularRef(childNode, dba);
+      if (circularNode != null)
+      {
+        context.createFailure(Validator.CIRCULAR_REFERENCE, childNode, 
+            "Circular reference to '" + dba.getName() + "'", 
+            new Fix("Modify parents of '" + child.getName() + "'", child),
+            new Fix("Modify parents of '" + dba.getName() + "'", dba)
+          );
+      }
+      else
+      {
+        Extract extract = getExtract(dba);
+        bioAssayNode = createItemNode(nf, dba, null, false, folderNode == null ? childNode : folderNode, ChildNodeDirection.REVERSE);
+        if (extract != null && bioAssayNode != null)
+        {
+          bioAssayNode.setAttribute(NodeAttribute.EXTRACT, extract);
+        }
+      }
+    }
+    postValidateFolder(nf, folderNode, childNode, bioAssayNode == null);
+    return folderNode == null ? bioAssayNode : folderNode;
+  }
+
+  /**
+    Get the extract that is associated with the current derived bioassay
+    @return The extract or null if none was found
+  */
+  private Extract getExtract(DerivedBioAssay bioAssay)
+  {
     Extract extract = null;
-    boolean denied = false;
     try
     {
-      bioAssay = child.getParent();
-      // We must clone/set the EXTRACT attribute so that upstream loaders
-      // follow the correct path when reaching the biomaterials section
-      extract = findExtract(childNode, bioAssay);
+      extract = bioAssay.getExtract();
     }
     catch (PermissionDeniedException ex)
-    {
-      denied = true;
-    }
-
-    Object cacheKey = new IndexedCacheKey(bioAssay, extract);
-    Node bioAssayNode = createItemNode(nf, bioAssay, cacheKey, denied, 
-        childNode, ChildNodeDirection.REVERSE);
-    if (extract != null && bioAssayNode != null)
-    {
-      bioAssayNode.setAttribute(NodeAttribute.EXTRACT, extract);
-    }
-    return bioAssayNode;
-  }
-
-  /**
-    Try to locate the extract we are following by first
-    checking if the node or any of it's parents have a
-    {@link NodeAttribute#EXTRACT} attribute set. If not we 
-    check if the current bioassay has an extract.
-    @return The extract or null if none was found
-  */
-  private Extract findExtract(Node node, DerivedBioAssay bioAssay)
-  {
-    Extract extract = null;
-    Node nodeWithExtract = node == null ? 
-        null : node.getFirstNode(new HasAttributeFilter(NodeAttribute.EXTRACT));
-    if (nodeWithExtract != null)
-    {
-      extract = nodeWithExtract.getAttribute(NodeAttribute.EXTRACT);
-    }
-    else
-    {
-      try
-      {
-        extract = bioAssay.getExtract();
-      }
-      catch (PermissionDeniedException ex)
-      {}
-    }
+    {}
     return extract;
   }
+  
+  private Set<Integer> getExtractChain(Node node)
+  {
+    List<Node> extractNodes = node.findAll(new ItemTypeFilter(Item.EXTRACT));
+    Set<Integer> extractIds = new HashSet<Integer>(extractNodes.size());
+    for (Node n : extractNodes)
+    {
+      extractIds.add(n.getItem().getId());
+    }
+    return extractIds;
+  }
+  
 }

trunk/src/core/net/sf/basedb/util/overview/loader/ExtractLoader.java

@@ -21 +21 @@
 */
 package net.sf.basedb.util.overview.loader;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import net.sf.basedb.core.BioMaterialList;
@@ -34 +38 @@
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
@@ -307 +312 @@
     Node folderNode = null;
     NodeFactory<Extract> nf = getNodeFactory(dc, context);
-  
-    // If we have followed this path from an item that has specified an extract
-    // we should only load that extract when following the path upstreams
-    Extract extract = null;
-    Node nodeWithExtract = bioAssayNode.getFirstNode(new HasAttributeFilter(NodeAttribute.EXTRACT));
-    if (nodeWithExtract != null)
-    {
-      extract = nodeWithExtract.getAttribute(NodeAttribute.EXTRACT);
-    }
-    
+
     ItemQuery<Extract> query = context.initQuery(bioAssay.getExtracts(0), "name");
-    if (extract != null) 
-    {
-      query.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(extract.getId())));
+
+    // If we have followed this path from derived bioassays that has specified an 
+    // extract we should only load the same extracts when following the path upstreams
+    Set<Integer> extractIds = getExtractChain(bioAssayNode);
+    if (extractIds.size() > 0) 
+    {
+      query.restrict(
+        Restrictions.in(Hql.property("id"), Expressions.parameter("extracts"))
+        );
+      query.setParameter("extracts", extractIds, Type.INT);
     }
     ItemResultIterator<Extract> it = query.iterate(dc);
     while (it.hasNext())
     {
-      extract = it.next();
+      Extract extract = it.next();
       if (folderNode == null)
       {
@@ -332 +335 @@
       createItemNode(nf, extract, extract, false, folderNode, ChildNodeDirection.REVERSE);
     }
-    postValidateFolder(nf, folderNode, bioAssayNode, nodeWithExtract == null);
+    postValidateFolder(nf, folderNode, bioAssayNode, extractIds.size() > 0);
     return folderNode;
   }
@@ -442 +445 @@
     
   }
+  
+  private Set<Integer> getExtractChain(Node node)
+  {
+    List<Node> nodesWithExtract = node.findAll(new HasAttributeFilter(NodeAttribute.EXTRACT));
+    Set<Integer> extractIds = new HashSet<Integer>(nodesWithExtract.size());
+    for (Node n : nodesWithExtract)
+    {
+      extractIds.add(n.getAttribute(NodeAttribute.EXTRACT).getId());
+    }
+    return extractIds;
+  }
+  
 }

trunk/src/core/net/sf/basedb/util/overview/loader/PhysicalBioAssayLoader.java

@@ -21 +21 @@
 */
 package net.sf.basedb.util.overview.loader;
+
+import java.util.List;
 
 import net.sf.basedb.core.ArraySlide;
@@ -33 +35 @@
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.util.overview.Node;
-import net.sf.basedb.util.overview.NodeAttribute;
 import net.sf.basedb.util.overview.OverviewContext;
 import net.sf.basedb.util.overview.OverviewUtil;
 import net.sf.basedb.util.overview.cache.IndexedCacheKey;
-import net.sf.basedb.util.overview.filter.HasAttributeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
 import net.sf.basedb.util.overview.node.NameableNameGenerator;
@@ -103 +103 @@
   {
     NodeFactory<PhysicalBioAssay> nf = getNodeFactory(dc, context);
-    PhysicalBioAssay bioAssay = null;
-    Extract extract = null;
-    boolean denied = false;
-    try
-    {
-      DerivedBioAssay bas = (DerivedBioAssay)derivedBioAssayNode.getItem(dc);
-      bioAssay = bas.getPhysicalBioAssay();
-      // We must clone/set the EXTRACT attribute so that upstream loaders
-      // follow the correct path when reaching the biomaterials section
-      Node nodeWithExtract = derivedBioAssayNode.getFirstNode(new HasAttributeFilter(NodeAttribute.EXTRACT));
-      if (nodeWithExtract != null)
-      {
-        extract = nodeWithExtract.getAttribute(NodeAttribute.EXTRACT);
-      }
-    }
-    catch (PermissionDeniedException ex)
-    {
-      denied = true;
-    }
-    Object cacheKey = new IndexedCacheKey(bioAssay, extract);
-    Node bioAssayNode = createItemNode(nf, bioAssay, cacheKey, denied, derivedBioAssayNode, ChildNodeDirection.REVERSE);
-    if (extract != null && bioAssayNode != null)
-    {
-      bioAssayNode.setAttribute(NodeAttribute.EXTRACT, extract);
-    }
-    return bioAssayNode;
+    DerivedBioAssay dba = (DerivedBioAssay)derivedBioAssayNode.getItem(dc);
+    
+    ItemQuery<PhysicalBioAssay> query = context.initQuery(dba.getPhysicalBioAssays(), "name");
+    List<PhysicalBioAssay> parents = query.list(dc);
+
+    Node folderNode = null;
+    Node bioAssayNode = null;
+    if (parents.size() > 1)
+    {
+      folderNode = new Node("parents", "Physical bioassays", derivedBioAssayNode, ChildNodeDirection.REVERSE);
+    }
+
+    for (PhysicalBioAssay pba : parents)
+    {
+      bioAssayNode = createItemNode(nf, pba, null, false, folderNode == null ? derivedBioAssayNode : folderNode, ChildNodeDirection.REVERSE);
+    }
+    postValidateFolder(nf, folderNode, derivedBioAssayNode, bioAssayNode == null);
+    return folderNode == null ? bioAssayNode : folderNode;
   }
   
@@ -230 +222 @@
     {
       PhysicalBioAssay bioAssay = it.next();
-      int position = bioAssay.getCreationEvent().getEventSource(extract).getPosition();
-      Object cacheKey = position == 0 ? bioAssay : new IndexedCacheKey(bioAssay, position);
+      Object cacheKey = new IndexedCacheKey(bioAssay, extract);
       if (folderNode == null)
       {

trunk/src/core/net/sf/basedb/util/overview/validator/DerivedBioAssayValidator.java

@@ -111 +111 @@
       }
     }
-    
+    /*
     // Check that parent items make sense
     DerivedBioAssay bioAssay = (DerivedBioAssay)node.getItem(dc);
@@ -158 +158 @@
       }
     }
+    */
   }